Methan molecule simulation

Hi guys,

I was trying to run simulation for methane molecules in nanotubes but I had an error message that all pair coeffs were not set in my model.

My data file and input script

a) running error

Reading data file …

orthogonal box = (-19.964 -20.0245 5.03305) to (80.036 79.9755 55.124)

1 by 1 by 1 MPI processor grid

reading atoms …

3700 atoms

scanning bonds …

4 = max bonds/atom

scanning angles …

3 = max angles/atom

scanning dihedrals …

8 = max dihedrals/atom

scanning impropers …

2 = max impropers/atom

reading bonds …

3770 bonds

reading angles …

3480 angles

reading dihedrals …

6870 dihedrals

reading impropers …

1140 impropers

Finding 1-2 1-3 1-4 neighbors …

special bond factors lj: 0 0 0

special bond factors coul: 0 0 0

4 = max # of 1-2 neighbors

6 = max # of 1-3 neighbors

18 = max # of 1-4 neighbors

18 = max # of special neighbors

500 atoms in group cnt

1000 atoms in group ch4

3700 atoms in group all

ERROR: All pair coeffs are not set (…/pair.cpp:228)

b) data file

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Tue Nov 28 21:55:27 +0900 2017

3700 atoms

3770 bonds

3480 angles

6870 dihedrals

1140 impropers

7 atom types

1 bond types

2 angle types

1 dihedral types

2 improper types

-19.963999 80.036001 xlo xhi

-20.024500 79.975500 ylo yhi

5.033046 55.123954 zlo zhi

Pair Coeffs

ERROR: All pair coeffs are not set (../pair.cpp:228)

:

7 atom types

I'd like to say I know the reason, but somehow I'm not seeing the
problem either.
Checking pair.cpp line 228:

  for (i = 1; i <= atom->ntypes; i++)
    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");

Either somehow LAMMPS thinks atom->ntypes is larger than 7, or it got
confused by these lines:

pair_coeff 1 6 0.03 2.5 #1H-C
pair_coeff 2 6 0.03 2.5 #2H-C
pair_coeff 3 6 0.03 2.5 #3H-C
pair_coeff 4 6 0.03 2.5 #4H-C

Curious: Did you place these lines before or after the other
pair_coeff commands in your script?

To help diagnose the problem, try replacing the code above with:

  for (i = 1; i <= atom->ntypes; i++) {
    fprintf(stderr,"i=%d, ntypes=%d\n");
    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
  }

compile LAMMPS, run your code, and let us know what you found.

Andrew

ERROR: All pair coeffs are not set (../pair.cpp:228)

:

7 atom types

I'd like to say I know the reason, but somehow I'm not seeing the
problem either.
Checking pair.cpp line 228:

  for (i = 1; i <= atom->ntypes; i++)
    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");

Either somehow LAMMPS thinks atom->ntypes is larger than 7, or it got
confused by these lines:

pair_coeff 1 6 0.03 2.5 #1H-C
pair_coeff 2 6 0.03 2.5 #2H-C
pair_coeff 3 6 0.03 2.5 #3H-C
pair_coeff 4 6 0.03 2.5 #4H-C

Curious: Did you place these lines before or after the other
pair_coeff commands in your script?

To help diagnose the problem, try replacing the code above with:

  for (i = 1; i <= atom->ntypes; i++) {
    fprintf(stderr,"i=%d, ntypes=%d\n");
    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
  }

ugh. My apologies. I meant to say:

  for (i = 1; i <= atom->ntypes; i++) {
    fprintf(stderr,"i=%d, ntypes=%d\n", i, atom->ntypes);
    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
  }